title: PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences.
abstract: BACKGROUND
  The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the identification of the few loci in the genome that can serve as unique markers for strain differentiation. PrimerSNP attempts to identify reliable strain-specific markers, on which specific primers are designed for pathogen detection purpose.
  
  
  RESULTS
  PrimerSNP is an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. The allele-specific primers could distinguish query sequences of one strain from other homologous sequences by standard PCR reaction. Additionally, PrimerSNP provides a feature for designing common primers that can amplify all the homologous sequences of multiple strains/species of microorganisms. PrimerSNP is freely available at http://cropdisease.ars.usda.gov/~primer.
  
  
  CONCLUSIONS
  PrimerSNP is a high-throughput specific primer generation tool for the differentiation of phylogenetically-related strains/species. Experimental validation showed that this software had a successful prediction rate of 80.4 - 100% for strain specific primer design.
authors.affiliation: Citrus Research Board, 323 W. Oak Street, Visalia, CA 93291, USA. jiqiangyao@yahoo.com
authors.forename: Jiqiang
authors.initials: J
authors.lastname: Yao
authors.forename: Hong
authors.initials: H
authors.lastname: Lin
authors.forename: Allen
authors.initials: A
authors.lastname: Van Deynze
authors.forename: Harshavardhan
authors.initials: H
authors.lastname: Doddapaneni
authors.forename: Martha
authors.initials: M
authors.lastname: Francis
authors.forename: Eliana Gertrudes Macedo
authors.initials: EG
authors.lastname: Lemos
authors.forename: Edwin L
authors.initials: EL
authors.lastname: Civerolo
mesh_terms: D000483:Alleles; D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D017931:DNA Primers / Q000235:genetics*; D016680:Genome, Bacterial; D020407:Internet; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D012984:Software
chemical_list: D017931:DNA Primers